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Neural-Retina-Atlas

This repository contains the scripts used for the paper 'A proteogenomic atlas of the human neural retina' by Riepe et al. (2024).

Data

Raw PacBio Iso-Seq data are available at the European Genome-phenome Archive (EGA) under accession number EGAD50000000101. The mass-spectromety proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE​​ partner repository with the dataset identifier PXD045187. Intermediate files generated during the analysis and reference files can be downloaded from Zenodo:

  • reference data: DOI
  • intermediate analysis files: DOI

The processed data is available as UCSC genome browser track (https://genome-euro.ucsc.edu/s/tabeariepe/retina_atlas).

Scripts

  • Data can be used to store the downloaded data from Zenodo to rerun the scripts
  • Figures and Tables contains scripts used to create the figures and tables
  • Proteomics contains all scripts used for the proteogenomic analysis
  • Transcriptomics contains all scripts for the Iso-Seq analysis
  • Retina specific exons describes how we looked for previous identified retina-specific exons in our PacBio dataset
  • Scripts contains small scripts and functions used for the analysis